BioTech最新文献

{"title":"CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data.","authors":"Haibo Liu, Kai Hu, Kevin O'Connor, Michelle A Kelliher, Lihua Julie Zhu","doi":"10.3390/biotech13030030","DOIUrl":"10.3390/biotech13030030","url":null,"abstract":"<p><p>RNA sequencing (RNA-seq) has become a standard method for profiling gene expression, yet genomic DNA (gDNA) contamination carried over to the sequencing library poses a significant challenge to data integrity. Detecting and correcting this contamination is vital for accurate downstream analyses. Particularly, when RNA samples are scarce and invaluable, it becomes essential not only to identify but also to correct gDNA contamination to maximize the data's utility. However, existing tools capable of correcting gDNA contamination are limited and lack thorough evaluation. To fill the gap, we developed CleanUpRNAseq, which offers a comprehensive set of functionalities for identifying and correcting gDNA-contaminated RNA-seq data. Our package offers three correction methods for unstranded RNA-seq data and a dedicated approach for stranded data. Through rigorous validation on published RNA-seq datasets with known levels of gDNA contamination and real-world RNA-seq data, we demonstrate CleanUpRNAseq's efficacy in detecting and correcting detrimental levels of gDNA contamination across diverse library protocols. CleanUpRNAseq thus serves as a valuable tool for post-alignment quality assessment of RNA-seq data and should be integrated into routine workflows for RNA-seq data analysis. Its incorporation into OneStopRNAseq should significantly bolster the accuracy of gene expression quantification and differential expression analysis of RNA-seq data.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348166/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Insight into the Response of Lactic Acid Bacteria to Bile Acids.","authors":"Caren N Moreno, Jorge N Gomez, María P Taranto, Ana E Ledesma, Ana Y Bustos","doi":"10.3390/biotech13030029","DOIUrl":"10.3390/biotech13030029","url":null,"abstract":"<p><p>Bile acids (BAs) are the main endogenous modulators of the composition and metabolic activity of the intestinal microbiota. In the present work, the effect of conjugated (glycodeoxycholic, glycocholic, taurodeoxycholic, taurocholic acids) and free BAs [cholic acid (CA) and deoxycholic acid (DCA)] on the survival, biological molecules, and structural and surface properties of two potential probiotic lactic acid bacteria (LAB) was evaluated. For this, viability assays, Raman spectroscopy, scanning electron microscopy (SEM), and zeta potential (ZP) measurements were employed. Our results evidenced that free BAs were more toxic than conjugates, with CA being significantly more harmful than deoxycholic acid (DCA). RAMAN studies show that BAs modify the bands corresponding to proteins, lipids, carbohydrates, and DNA. SEM showed that BAs cause surface distortions with depressions and fold formation, as well as incomplete cell division. DCA was the one that least altered the ZP of bacteria when compared to CA and taurodeoxycholic acid, with gradual changes towards more positive values. In general, the magnitude of these effects was different according to the BA and its concentration, being more evident in the presence of CA, even at low concentrations, which would explain its greater inhibitory effect. This work provides solid evidence on the effects of BAs on LAB that will allow for the development of strategies by which to modulate the composition of the microbiota positively.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Removal of Cadmium (II) from Aqueous Solution Using <i>Galdieria sulphuraria</i> CCMEE 5587.1.","authors":"Hari Lal Kharel, Lina Jha, Melissa Tan, Thinesh Selvaratnam","doi":"10.3390/biotech13030028","DOIUrl":"10.3390/biotech13030028","url":null,"abstract":"<p><p>The release of cadmium into the environment is a significant global concern due to its toxicity, non-biodegradability, and persistence in nature. There is an urgent need for effective, eco-friendly, and cost-effective systems for removing Cd because of the many drawbacks of conventional physicochemical techniques. This study investigated the ability of the extremophile red microalgal strain <i>Galdieria sulphuraria</i> CCMEE 5587.1 to tolerate and remove Cd (II) ions at acidic pH in a controlled laboratory environment. Three distinct concentrations of Cd (1.5 mg L^-1, 3 mg L^-1, and 6 mg L^-1) were introduced to the cyanidium medium, and <i>G. sulphuraria</i> cells were introduced in the medium and grown for ten days. Four distinct aspects were identified regarding Cd removal: time course Cd removal, total Cd removal, extracellular Cd removal, and intracellular Cd removal. The inhibitory effects of Cd on <i>G. sulphuraria</i> growth were observed using a daily growth profile. Initial incubation days showed an inhibition of <i>G. sulphuraria</i> growth. In addition, increasing the Cd concentration in the medium decreased the growth rate of <i>G. sulphuraria</i>. Rapid Cd removal occurred on the first day of the experiment, followed by a steady removal of Cd until the last day. The highest total removal efficiency occurred in a medium containing 3 mg L^-1 of Cd ions, which was 30%. In contrast, the highest sorption capacity occurred in a medium containing 6 mg L^-1 of Cd ions, which was 1.59 mg g^-1 of dry biomass. In all media compositions, a major fraction (>80%) of Cd removal occurred via adsorption on the cell surface (extracellular). These results showed that <i>G. sulphuraria</i> cells can remove Cd ions from aqueous solution, which makes them a potential bioremediation option for heavy metal removal.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11348382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142074067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydroponics with Microalgae and Cyanobacteria: Emerging Trends and Opportunities in Modern Agriculture.","authors":"Prabhaharan Renganathan, Edgar Omar Rueda Puente, Natalia V Sukhanova, Lira A Gaysina","doi":"10.3390/biotech13030027","DOIUrl":"10.3390/biotech13030027","url":null,"abstract":"<p><p>The global population is expected to reach 9.5 billion, which means that crop productivity needs to double to meet the growing population's food demand. Soil degradation and environmental factors, such as climate events, significantly threaten crop production and global food security. Furthermore, rapid urbanization has led to 55% of the world's population migrating to cities, and this proportion is expected to increase to 75% by 2050, which presents significant challenges in producing staple foods through conventional hinterland farming. Numerous studies have proposed various sustainable farming techniques to combat the shortage of farmable land and increase food security in urban areas. Soilless farming techniques such as hydroponics have gained worldwide popularity due to their resource efficiency and production of superior-quality fresh products. However, using chemical nutrients in a conventional hydroponic system can have significant environmental impacts, including eutrophication and resource depletion. Incorporating microalgae into hydroponic systems as biostimulants offers a sustainable and ecofriendly approach toward circular bioeconomy strategies. The present review summarizes the plant growth-promoting activity of microalgae as biostimulants and their mechanisms of action. We discuss their effects on plant growth parameters under different applications, emphasizing the significance of integrating microalgae into a closed-loop circular economy model to sustainably meet global food demands.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11270261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141761416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of Critical Parameters on the Extraction of Concentrated C-PE from Thermotolerant Cyanobacteria.","authors":"Ariadna H Vergel-Suarez, Janet B García-Martínez, German L López-Barrera, Néstor A Urbina-Suarez, Andrés F Barajas-Solano","doi":"10.3390/biotech13030021","DOIUrl":"10.3390/biotech13030021","url":null,"abstract":"<p><p>This work aimed to identify the influence of pH, molarity, <i>w</i>/<i>v</i> fraction, extraction time, agitation, and either a sodium (Na₂HPO₄·7H₂O-NaH₂PO₄·H₂O) or potassium buffer (K₂HPO₄-KH₂PO₄) used in the extraction of C-phycoerythrin (C-PE) from a thermotolerant strain of <i>Potamosiphon</i> sp. An experimental design (Minimum Run Resolution V Factorial Design) and a Central Composite Design (CCD) were used. According to the statistical results of the first design, the K-PO₄ buffer, pH, molarity, and <i>w</i>/<i>v</i> fraction are vital factors that enhance the extractability of C-PE. The construction of a CCD design of the experiments suggests that the potassium phosphate buffer at pH 5.8, longer extraction times (50 min), and minimal extraction speed (1000 rpm) are ideal for maximizing C-PE concentration, while purity is unaffected by the design conditions. This optimization improves extraction yields and maintains the desired bright purple color of the phycobiliprotein.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 3","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11270330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141761417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico and In Vitro Evaluation of the Antifungal Activity of a New Chromone Derivative against <i>Candida</i> spp.","authors":"Gleycyelly Rodrigues Araújo, Palloma Christine Queiroga Gomes da Costa, Paula Lima Nogueira, Danielle da Nóbrega Alves, Alana Rodrigues Ferreira, Pablo R da Silva, Jéssica Cabral de Andrade, Natália F de Sousa, Paulo Bruno Araujo Loureiro, Marianna Vieira Sobral, Damião P Sousa, Marcus Tullius Scotti, Ricardo Dias de Castro, Luciana Scotti","doi":"10.3390/biotech13020016","DOIUrl":"10.3390/biotech13020016","url":null,"abstract":"<p><p><i>Candida</i> species are frequently implicated in the development of both superficial and invasive fungal infections, which can impact vital organs. In the quest for novel strategies to combat fungal infections, there has been growing interest in exploring synthetic and semi-synthetic products, particularly chromone derivatives, renowned for their antimicrobial properties. In the analysis of the antifungal activity of the compound (<i>E</i>)-benzylidene-chroman-4-one against <i>Candida</i>, in silico and laboratory tests were performed to predict possible mechanisms of action pathways, and in vitro tests were performed to determine antifungal activity (MIC and MFC), to verify potential modes of action on the fungal cell membrane and wall, and to assess cytotoxicity in human keratinocytes. The tested compound exhibited predicted affinity for all fungal targets, with the highest predicted affinity observed for thymidylate synthase (-102.589 kJ/mol). MIC and CFM values ranged from 264.52 μM (62.5 μg/mL) to 4232.44 μM (1000 μg/mL). The antifungal effect likely occurs due to the action of the compound on the plasma membrane. Therefore, (E)-benzylidene-chroman-4-one showed fungicidal-like activity against <i>Candida</i> spp., possibly targeting the plasma membrane.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11201913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141451795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteases: Importance, Immobilization Protocols, Potential of Activated Carbon as Support, and the Importance of Modifying Supports for Immobilization.","authors":"Mateus Pereira Flores Santos, Evaldo Cardozo de Souza Junior, Carolina Villadóniga, Diego Vallés, Susana Castro-Sowinski, Renata Cristina Ferreira Bonomo, Cristiane Martins Veloso","doi":"10.3390/biotech13020013","DOIUrl":"10.3390/biotech13020013","url":null,"abstract":"<p><p>Although enzymes have been used for thousands of years, their application in industrial processes has gained importance since the 20th century due to technological and scientific advances in several areas, including biochemistry [...].</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11130871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eco-Friendly Sanitization of Indoor Environments: Effectiveness of Thyme Essential Oil in Controlling Bioaerosol Levels and Disinfecting Surfaces.","authors":"Daniela Sateriale, Giuseppina Forgione, Giuseppa Anna De Cristofaro, Leonardo Continisio, Chiara Pagliuca, Roberta Colicchio, Paola Salvatore, Marina Paolucci, Caterina Pagliarulo","doi":"10.3390/biotech13020012","DOIUrl":"10.3390/biotech13020012","url":null,"abstract":"<p><p>Bioaerosols and pathogens in indoor workplaces and residential environments are the primary culprits of several infections. Techniques for sanitizing air and surfaces typically involve the use of UV rays or chemical sanitizers, which may release chemical residues harmful to human health. Essential oils, natural substances derived from plants, which exhibit broad antimicrobial properties, could be a viable alternative for air and surface sanitation. The objective of this study has been to investigate the efficacy of thyme essential oil (TEO) in environmental sanitation processes. In Vitro assays through agar well diffusion, disk volatilization and tube dilution methods revealed significant antimicrobial activity of TEO 100% against foodborne and environmental isolates, with both bacteriostatic/fungistatic and bactericidal/fungicidal effects. Therefore, aqueous solutions of TEO 2.5% and 5% were formulated for air sanitation through nebulization and surface disinfection via direct contact. Bioaerosol samples and surface swabs were analyzed before and after sanitation, demonstrating the efficacy of aqueous solutions of TEO in reducing mesophilic and psychrophilic bacteria and environmental fungi levels in both air and on surfaces. The obtained results prove the antimicrobial potential of aqueous solutions of TEO in improving indoor air quality and surface cleanliness, suggesting thyme essential oil as an effective and safe natural sanitizer with minimal environmental impact compared to dangerous chemical disinfectants.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11130963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of the 12-Base Short Dimeric Myogenetic Oligodeoxynucleotide That Induces Myogenic Differentiation.","authors":"Koji Umezawa, Rena Ikeda, Taiichi Sakamoto, Yuya Enomoto, Yuma Nihashi, Sayaka Shinji, Takeshi Shimosato, Hiroshi Kagami, Tomohide Takaya","doi":"10.3390/biotech13020011","DOIUrl":"10.3390/biotech13020011","url":null,"abstract":"<p><p>A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5'-AGA TTA GGG TGA GGG TGA-3'), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining its structure-based function is a major challenge. Here, we report the novel 12-base non-telomeric myoDN, iMyo01 (5'-TTG GGT GGG GAA-3'), which has comparable myogenic activity to iSN04. iMyo01 as well as iSN04 promoted myotube formation of primary-cultured human myoblasts with upregulation of myogenic gene expression. Both iMyo01 and iSN04 interacted with nucleolin, but iMyo01 did not bind to berberine, the isoquinoline alkaloid that stabilizes iSN04. Nuclear magnetic resonance revealed that iMyo01 forms a G-quadruplex structure despite its short sequence. Native polyacrylamide gel electrophoresis and a computational molecular dynamics simulation indicated that iMyo01 forms a homodimer to generate a G-quadruplex. These results provide new insights into the aptamer truncation technology that preserves aptamer conformation and bioactivity for the development of efficient nucleic acid drugs.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11130974/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141158485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Susceptibility of <i>Tetranychus urticae</i> to the Alkaloidal Extract of <i>Zanthoxylum schreberi</i> Bark: Phenotypic and Biochemical Insights for Biotechnological Exploitation.","authors":"Ricardo A Rincón, Daniel Rodríguez, Ericsson Coy-Barrera","doi":"10.3390/biotech13010005","DOIUrl":"10.3390/biotech13010005","url":null,"abstract":"<p><p><i>Tetranychus urticae</i> Koch, a phytophagous mite, is one of the most significant crop pests globally. The primary method employed for controlling <i>T. urticae</i> involves chemical means, utilizing synthesized products, posing the risk of developing resistance. The urgency for novel strategies integrated into pest management programs to combat this mite is becoming increasingly imperative. Botanical pesticides emerge as a promising tool to forestall arthropod resistance. Among these, extracts from Rutaceae plants, abundant in bioactive specialized metabolites, have demonstrated potential as insecticides and miticides. In this study, various concentrations of alkaloidal extracts sourced from the bark of <i>Zanthoxylum schreberi</i> J.F.Gmel. (Rutaceae) were evaluated against <i>T. urticae</i> adult females. Furthermore, the extract's combination with three distinct commercial acaricides (i.e., chlorfenapyr, cyflumetofen, and abamectin) was also assessed for this mite. Chemical characterization of the extract via LC-MS allowed for the annotation of various compounds related to ten benzylisoquinoline-derived alkaloids. The extract, both alone and in combination with commercial insecticides, yielded varying responses, inducing over 40% mortality at 2% <i>w</i>/<i>w</i>, demonstrating a 90% repellency rate at the same concentration, and exerting a moderate impact on fecundity. These treatments extended beyond phenotypic responses, delving into the biochemical effects on treated <i>T. urticae</i> females through an exploration of the impact on four enzymes, i.e., acetylcholinesterase (AChE), glutathione <i>S</i>-transferase (GST), esterases (GE), and P450-like monooxygenases (PMO). Employing consensus docking studies and in vitro enzymatic evaluations, it was discovered that the <i>Z. schreberi</i>-derived extract and its constituents significantly affected two key enzymes, AChE and GST (IC₅₀ < 6 µM), which were associated with the phenotypic observations of <i>T. urticae</i> females. The evaluation of alkaloid-rich botanicals showcases promising potential as a relevant biotechnological strategy in addressing mite-related concerns, offering a pathway toward innovative and sustainable pest management solutions.</p>","PeriodicalId":34490,"journal":{"name":"BioTech","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10885115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139933216","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}